structural-biology

Structural Biology

Version Compatibility

Reference examples assume:

• biopython 1.84+
• AlphaFold DB public API current format
• optional visualization stack such as py3Dmol or PyMOL

Verify before use:

• Python: python -c "import Bio; print(Bio.__version__)"

Overview

Use this skill when the task is:

• retrieving AlphaFold-predicted structures by UniProt accession
• downloading coordinate and confidence files
• reading pLDDT or PAE to judge confidence
• mapping sequence findings onto structure

When To Use This Skill

• a UniProt accession or known protein target exists
• experimental structure is absent or incomplete
• the user needs confidence-aware structural interpretation

Quick Route

• known UniProt accession: query AlphaFold DB first
• novel designed sequence without AlphaFold DB entry: use a separate prediction workflow such as ColabFold
• structure interpretation request: always inspect pLDDT and PAE before making mechanistic claims

Progressive Disclosure

• Read technical_reference.md for confidence interpretation and source-selection rules.
• Read commands_and_thresholds.md for AlphaFold DB retrieval patterns, URL layouts, and file conventions.

Expected Inputs

• UniProt accession or sequence context
• optional residue list, mutation list, or ligand site hypothesis

Expected Outputs

• results/structures/AF-<accession>.cif
• results/structures/AF-<accession>.pdb
• results/confidence/AF-<accession>-confidence.json
• results/confidence/AF-<accession>-pae.json
• figures/AF-<accession>-pae.png

Starter Pattern

from Bio.PDB import alphafold_db

prediction = next(alphafold_db.get_predictions("P00520"))
cif_path = alphafold_db.download_cif_for(prediction, directory="results/structures")
print(cif_path)

Confidence Thresholds

pLDDT

pLDDT	Interpretation
> 90	very high confidence
70-90	good backbone confidence
50-70	low confidence
< 50	likely disorder or unreliable local structure